GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LAT2 in Caldicellulosiruptor hydrothermalis 108

Align Serine/threonine exchanger SteT (characterized)
to candidate WP_013403835.1 CALHY_RS10010 amino acid permease

Query= SwissProt::O34739
         (438 letters)



>NCBI__GCF_000166355.1:WP_013403835.1
          Length = 436

 Score =  313 bits (801), Expect = 9e-90
 Identities = 167/430 (38%), Positives = 254/430 (59%), Gaps = 4/430 (0%)

Query: 8   LKKEIGLLFALTLVIGTIIGSGVFMKPGAVLAYSGDSKMALFAWLLGGILTLAGGLTIAE 67
           LKK + +  AL+LV+G +IGSGVF K   V  YSG      FAWLLGG+++L G L  AE
Sbjct: 7   LKKNLNIWMALSLVVGMVIGSGVFFKATPVAKYSGSFAFIFFAWLLGGVMSLCGALVAAE 66

Query: 68  IGTQIPKTGGLYTYLEEVYGEFWGFLCGWVQIIIYGPAIIGALGLYFGSLMANLFGWGSG 127
              + P TGGLY YLE++YG    FL GW+  +IY PAI+ AL + F   ++++      
Sbjct: 67  FSARYPHTGGLYVYLEKIYGNEISFLFGWMNTLIYTPAILSALSVLFADQVSSMLNANQM 126

Query: 128 LSKVIGIIAVLFLCVINIIGTKYGGFVQTLTTIGKLIPIACIIVFGLWKG-DQHIFTAVN 186
           +  ++ +  +  + +IN+IG KYGG +Q L T+ KLIP+  II+FGL +  +   F +  
Sbjct: 127 VHDILVLSILTAIVIINVIGNKYGGALQLLATVLKLIPLFLIILFGLIRPIEAENFASYG 186

Query: 187 ESISDMNFGAAILATLFAYDGWILLAALGGEMKNPEKLLPRAMTGGLLIVTAIYIFINFA 246
                 NFG A+L+TL+AYDGW+ +  + GEMKN +K L   +  G+L V  +Y+ +N A
Sbjct: 187 HFTK--NFGLAVLSTLWAYDGWLSVPNVAGEMKNAKKNLVLVLIFGMLFVIVVYLLVNIA 244

Query: 247 LLHILSANEIVTLGENATSTAATMLFGSIGGKLISVGIIVSIFGCLNGKVLSFPRVSFAM 306
            ++++   ++ T  ENA +  +  LFG IG  LIS+GII+SI G LNG  L+  R+ +AM
Sbjct: 245 YINVIGIGKLAT-AENAINLISEKLFGQIGKVLISLGIIISIVGTLNGFALTGIRIPYAM 303

Query: 307 AERKQLPFAEKLSHVHPSFRTPWIAISFQIALALIMMLISNPDKLSEISIFMIYIFYVMA 366
           A  ++       S +HP F TP  +      L+L+ +   + ++L+++++F  +IFYV+ 
Sbjct: 304 ATNQRFIVNNVFSKLHPRFATPVNSSILVYILSLLYIFTRSFNRLTDLAMFSTWIFYVLF 363

Query: 367 FFAVFILRKRAKGEKRAYSVPLYPFMPILAIAGSFFVLGSTLITDTMSCGLSILIGLAGL 426
           F  +FI RKR    K  Y+  LYP  P++AI    ++L + +  +      SILI L GL
Sbjct: 364 FIGIFIKRKREGKNKEGYNTFLYPITPLVAIFSGLYILVNNIFLNPTDSIFSILITLLGL 423

Query: 427 PVYYGMKKRK 436
           PVY+   K+K
Sbjct: 424 PVYFLFVKKK 433


Lambda     K      H
   0.328    0.145    0.437 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 649
Number of extensions: 35
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 438
Length of database: 436
Length adjustment: 32
Effective length of query: 406
Effective length of database: 404
Effective search space:   164024
Effective search space used:   164024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory